Can you try to switch off the application preference to show warnings as dialogs: Edit - Application Preferences - Widgets - Command Line - [ ] Show warnings as dialog (make sure that option is NOT checked).
This option might cause problems with warnings produced when drawings are loaded since you might have to click away a lot of dialogs. I'll look into options to fix this problem for the next release.
Two solutions come to mind: 1) A checkbox to supress further popups for the active action 2) repetitions aware journal - Unix syslog does like this, eg sometimes it logs: "Last message repeated 25 times".
Simplest way was to just remember the last message and only show the current one, if different from the last one. Probably increment a counter for each occurence. This may still swamp the user though if eg. two different messages alternate.
Another way, store any messages into an object with a counter and only ever show the popup with a liste of messages in the end of an action.